RUST error when phasing with SV VCF file #7
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Hello, Before touching on the error, I do want to mention that we're only officially supporting As for the error itself, it appears to be failing a sanity check we have built into the tool. In particular, this sanity check compares the reference allele in the VCF (left: Matt |
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I'm going to close this for now, feel free to re-open if something changes with respect to the issue. |
holtjma
added
question
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Hi Matt, I saw a similar error when running the hiphase with a joint pbsv, pav and sniffles call. Here is the error:
Is this because the hiphase doesn't support the sniffles or pav output? Thanks, Hang Su |
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I suspect the answer to your question is yes. If you update to the latest version of HiPhase, this error should become clearer. Regardless, we do not currently support sniffles or pav due to some incomplete SV calls. |
Thanks for your reply Matt! If the assertion is checking the left reference allele is identical to the right reference sequence in the fasta file, does it require everything in the reference allele be upper case? We are trying to clean up the vcf files to fit into the Hiphase pipeline. Your help is much appreciated! Thanks, Hang |
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The reference genome sequences from the reference FASTA file will get converted to upper-case. I don't think we've seen an example where the VCF file did contained lower-case characters, so I suspect you will need to make those conversions yourself for the moment. I recommend doing both the reference and alternate alleles, otherwise you will likely get undefined behavior. |
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Yes, there are lower cases in vcf files... Will manually change the lower
cases into upper cases to see how things going. Thank you so much!
Hang
…On Tue, Jan 30, 2024 at 2:33 PM Matt Holt ***@***.***> wrote:
The reference genome sequences from the reference FASTA file will get
converted to upper-case.
I don't think we've seen an example where the VCF file did contained
lower-case characters, so I suspect you will need to make those conversions
yourself for the moment. I recommend doing both the reference and alternate
alleles, otherwise you will likely get undefined behavior.
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I am facing a
RUSTproblem when providingHiPhasewith a Structural Variants (SV)VCFfile to improve the phasing. Phasing works fine when only a Single Nucleotide Variants (SNV)VCFfile is provided. This is the command I am using:/path/hiphase-v0.8.0-x86_64-unknown-linux-gnu/hiphase -t 16 -r /path/ref.fa -b /path/sample.bam -p sample.haplotagged.bam -c /path/SNV.vcf.gz -o sample.SNV.phased.vcf.gz -c /path/SV.vcf.gz -o sample.SV.phased.vcf.gz -s sampleAnd this is the error:
The
SVVCFfile has been generated with[Sniffles2](https://github.com/fritzsedlazeck/Sniffles). We thought it might be related to Breakends (BND) variants but the error also appears when these are filtered out.Thanks in advance for looking into this :)
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